Merge pull request #183 from Steinbeck-Lab/dev-kohulan

feat: Add tests for chem router #181

tests/test_chem.py

@@ -0,0 +1,165 @@
+import pytest
+from fastapi.testclient import TestClient
+from app.main import app
+
+client = TestClient(app)
+
+
+@pytest.fixture
+def test_smiles():
+    return "CN1C=NC2=C1C(=O)N(C(=O)N2C)C"
+
+
+def test_chem_index():
+    response = client.get("/v1/chem/")
+    assert response.status_code == 200
+    assert response.json() == {"module": "chem", "message": "Successful", "status": 200}
+
+
+def test_smiles_to_stereo_isomers(test_smiles):
+    response = client.get(f"/v1/chem/stereoisomers?smiles={test_smiles}")
+    assert response.status_code == 200
+    assert response.headers["content-type"] == "application/json"
+    assert response.text == '["Cn1c(=O)c2c(ncn2C)n(C)c1=O"]'
+
+
+def test_SMILES_Descriptors_returns_descriptors(test_smiles):
+    response = client.get(f"/v1/chem/descriptors?smiles={test_smiles}")
+    assert response.status_code == 200
+    assert response.headers["content-type"] == "application/json"
+    assert (
+        response.text
+        == '{"atom_count":24,"heavy_atom_count":14,"molecular_weight":194.19,"exactmolecular_weight":194.08038,"alogp":-1.03,"rotatable_bond_count":0,"topological_polar_surface_area":61.82,"hydrogen_bond_acceptors":6,"hydrogen_bond_donors":0,"hydrogen_bond_acceptors_lipinski":6,"hydrogen_bond_donors_lipinski":0,"lipinski_rule_of_five_violations":0,"aromatic_rings_count":2,"qed_drug_likeliness":0.54,"formal_charge":0,"fractioncsp3":0.375,"number_of_minimal_rings":2,"linear_sugars":false,"circular_sugars":false,"murko_framework":"N1=C[N]C2=C1NCNC2","nplikeliness":-1.09}'
+    )
+
+    response = client.get(f"/v1/chem/descriptors?smiles={test_smiles}&format=html")
+    assert response.status_code == 200
+    assert response.headers["content-type"] == "text/html; charset=utf-8"
+
+    response = client.get("/v1/chem/descriptors")
+    assert response.status_code == 422  # Missing required parameter
+
+    response = client.get(f"/v1/chem/descriptors?smiles={test_smiles}&toolkit=unknown")
+    assert response.status_code == 200
+    assert response.headers["content-type"] == "application/json"
+    assert response.text == '"Error Calculating Descriptors"'
+
+
+@pytest.mark.parametrize(
+    "smiles, expected_score",
+    [
+        ("CN1C=NC2=C1C(=O)N(C(=O)N2C)C", "-1.09"),
+        ("CC=O", "0.96"),
+    ],
+)
+def test_NPlikeliness_Score(smiles, expected_score):
+    response = client.get(f"/v1/chem/npscore?smiles={smiles}")
+    assert response.status_code == 200
+    assert response.headers["content-type"] == "application/json"
+    assert response.json() == expected_score
+
+
+def test_ClassyFire_Classify(test_smiles):
+    response = client.get(f"/v1/chem/classyfire/classify?smiles={test_smiles}")
+    assert response.status_code == 200
+    assert response.headers["content-type"] == "application/json"
+
+
+@pytest.mark.parametrize(
+    "smiles, expected",
+    [("invalid_smiles", '"Error reading SMILES string, check again."')],
+)
+def test_cdk2d_coordinates(smiles, expected):
+    response = client.get(f"/v1/chem/cdk2d?smiles={smiles}")
+    assert response.status_code == 200
+    assert response.text == expected
+
+
+@pytest.mark.parametrize(
+    "smiles, expected",
+    [
+        (
+            "CC",
+            """     RDKit          3D\n'\n '\n'\n '  8  7  0  0  0  0  0  0  0  0999 V2000\n'\n '    0.7480   -0.0676    0.0869 C   0  0  0  0  0  0  0  0  0  0  0  0\n'\n '   -0.7480    0.0676   -0.0869 C   0  0  0  0  0  0  0  0  0  0  0  0\n'\n '    1.2303   -0.2658   -0.8749 H   0  0  0  0  0  0  0  0  0  0  0  0\n'\n '    1.1714    0.8520    0.5016 H   0  0  0  0  0  0  0  0  0  0  0  0\n'\n '    0.9830   -0.8922    0.7665 H   0  0  0  0  0  0  0  0  0  0  0  0\n'\n '   -0.9830    0.8922   -0.7665 H   0  0  0  0  0  0  0  0  0  0  0  0\n'\n '   -1.2303    0.2658    0.8749 H   0  0  0  0  0  0  0  0  0  0  0  0\n'\n '   -1.1714   -0.8520   -0.5016 H   0  0  0  0  0  0  0  0  0  0  0  0\n'\n '  1  2  1  0\n'\n '  1  3  1  0\n'\n '  1  4  1  0\n'\n '  1  5  1  0\n'\n '  2  6  1  0\n'\n '  2  7  1  0\n'\n '  2  8  1  0\n'\n 'M  END""",
+        ),
+        ("invalid_smiles", '"Error reading SMILES string, check again."'),
+    ],
+)
+def test_rdkit3d_mol(smiles, expected):
+    response = client.get(f"/v1/chem/rdkit3d?smiles={smiles}")
+    assert response.status_code == 200
+    # assert response.text == expected
+
+
+@pytest.mark.parametrize(
+    "smiles, toolkit, expected",
+    [
+        ("CC,CC", "cdk", '"1.00000"'),
+        ("CC,CC", "rdkit", "1.0"),
+        (
+            "CC,CC,CC",
+            "cdk",
+            "<table><tr><th></th><th>0</th><th>1</th><th>2</th></tr><tr><td>0</td><td>1.00000</td><td>1.00000</td><td>1.00000</td></tr><tr><td>1</td><td>1.00000</td><td>1.00000</td><td>1.00000</td></tr><tr><td>2</td><td>1.00000</td><td>1.00000</td><td>1.00000</td></tr></table>",
+        ),
+    ],
+)
+def test_tanimoto_similarity(smiles, toolkit, expected):
+    response = client.get(f"/v1/chem/tanimoto?smiles={smiles}&toolkit={toolkit}")
+    assert response.status_code == 200
+    assert response.text == expected
+
+
+@pytest.mark.parametrize(
+    "smiles, generator, width, height, rotate, CIP, unicolor",
+    [
+        ("CCO", "cdksdg", 512, 512, 0, False, False),
+        ("CCO", "rdkit", 512, 512, 0, False, False),
+    ],
+)
+def test_depict2D_molecule(smiles, generator, width, height, rotate, CIP, unicolor):
+    response = client.get(
+        f"/v1/chem/depict?smiles={smiles}&generator={generator}&width={width}&height={height}&rotate={rotate}&CIP={CIP}&unicolor={unicolor}"
+    )
+    assert response.status_code == 200
+    assert response.headers["content-type"] == "image/svg+xml"
+
+
+@pytest.mark.parametrize(
+    "smiles, fix, expected",
+    [
+        ("CCO", False, '"No Errors Found"'),
+        ("CCO", True, '"No Errors Found"'),
+    ],
+)
+def test_check_errors(smiles, fix, expected):
+    response = client.get(f"/v1/chem/checkerrors?smiles={smiles}&fix={fix}")
+    assert response.status_code == 200
+    assert response.headers["content-type"] == "application/json"
+    assert response.text == expected
+
+
+def test_depict3D_molecule(test_smiles):
+    response = client.get(f"/v1/chem/depict3D?smiles={test_smiles}")
+    assert response.status_code == 200
+    assert response.headers["content-type"] == "text/html; charset=utf-8"
+
+
+"""
+def test_hose_codes(test_smiles):
+    response = client.get(f"/v1/chem/hosecode?framework=cdk&smiles={test_smiles}")
+    assert response.status_code == 200
+    assert response.headers["content-type"] == "application/json"
+    assert response.text  == 
+    # Add more assertions for the expected response data
+"""
+
+
+def test_coconut_preprocessing(test_smiles):
+    response = client.get(f"/v1/chem/coconutpreprocessing?smiles={test_smiles}")
+    assert response.status_code == 200
+    assert response.headers["content-type"] == "application/json"
+
+
+# Run the tests
+if __name__ == "__main__":
+    pytest.main()

tests/test_converters.py

@@ -34,29 +34,40 @@ def test_SMILES_Canonicalise():
     )
     assert response.status_code == 200
     assert response.headers["content-type"] == "application/json"
+    assert response.text == '"Cn1c(=O)c2c(ncn2C)n(C)c1=O"'
 
 
 def test_SMILES_to_InChI():
     response = client.get("/v1/convert/inchi?smiles=CN1C=NC2=C1C(=O)N(C(=O)N2C)C")
     assert response.status_code == 200
     assert response.headers["content-type"] == "application/json"
+    assert (
+        response.text
+        == '"InChI=1S/C8H10N4O2/c1-10-4-9-6-5(10)7(13)12(3)8(14)11(6)2/h4H,1-3H3"'
+    )
 
 
 def test_SMILES_to_InChIKey():
     response = client.get("/v1/convert/inchikey?smiles=CN1C=NC2=C1C(=O)N(C(=O)N2C)C")
     assert response.status_code == 200
     assert response.headers["content-type"] == "application/json"
+    assert response.text == '"RYYVLZVUVIJVGH-UHFFFAOYSA-N"'
 
 
 def test_SMILES_to_CXSMILES():
     response = client.get("/v1/convert/cxsmiles?smiles=CN1C=NC2=C1C(=O)N(C(=O)N2C)C")
     assert response.status_code == 200
     assert response.headers["content-type"] == "application/json"
+    assert (
+        response.text
+        == '"CN1C=NC2=C1C(=O)N(C)C(=O)N2C |(2.68,2.45,;2.22,1.02,;3.1,-0.19,;2.22,-1.4,;0.8,-0.94,;0.8,0.56,;-0.5,1.31,;-0.5,2.81,;-1.8,0.56,;-3.1,1.31,;-1.8,-0.94,;-3.1,-1.69,;-0.5,-1.69,;-0.5,-3.19,)|"'
+    )
 
 
 def test_SMILES_convert_to_Formats():
     response = client.get("/v1/convert/formats?smiles=CN1C=NC2=C1C(=O)N(C(=O)N2C)C")
     assert response.status_code == 200
+    assert response.headers["content-type"] == "application/json"
     assert response.json() == {
         "mol": "\n     RDKit          2D\n\n 14 15  0  0  0  0  0  0  0  0999 V2000\n    2.7760    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    1.2760    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n    0.3943    1.2135    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.0323    0.7500    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.0323   -0.7500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.3943   -1.2135    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.7062   -2.6807    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    2.1328   -3.1443    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.4086   -3.6844    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.8351   -3.2209    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -2.9499   -4.2246    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n   -2.1470   -1.7537    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n   -3.5736   -1.2902    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.0967   -5.1517    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  1  2  1  0\n  2  3  1  0\n  3  4  2  0\n  4  5  1  0\n  5  6  2  0\n  6  7  1  0\n  7  8  2  0\n  7  9  1  0\n  9 10  1  0\n 10 11  2  0\n 10 12  1  0\n 12 13  1  0\n  9 14  1  0\n  6  2  1  0\n 12  5  1  0\nM  END\n",
         "cannonicalsmiles": "CN1C(=O)C2=C(N=CN2C)N(C)C1=O",
@@ -68,6 +79,7 @@ def test_SMILES_convert_to_Formats():
 def test_SMILES_to_IUPACname():
     response = client.get("/v1/convert/iupac?smiles=CN1C=NC2=C1C(=O)N(C(=O)N2C)C")
     assert response.status_code == 200
+    assert response.headers["content-type"] == "application/json"
     assert response.text == '"1,3,7-trimethylpurine-2,6-dione"'
 
 
@@ -76,18 +88,21 @@ def test_IUPACname_or_SELFIES_to_SMILES():
         "/v1/convert/smiles?input_text=1,3,7-trimethylpurine-2,6-dione&representation=iupac"
     )
     assert response.status_code == 200
+    assert response.headers["content-type"] == "application/json"
     assert response.text == '"CN1C=NC2=C1C(=O)N(C)C(=O)N2C"'
 
     response = client.get(
         "/v1/convert/smiles?input_text=[C][N][C][=N][C][=C][Ring1][Branch1][C][=Branch1][C][=O][N][Branch1][=Branch2][C][=Branch1][C][=O][N][Ring1][Branch2][C][C]&representation=selfies"
     )
     assert response.status_code == 200
+    assert response.headers["content-type"] == "application/json"
     assert response.text == '"CN1C=NC2=C1C(=O)N(C(=O)N2C)C"'
 
 
 def test_encode_SELFIES():
     response = client.get("/v1/convert/selfies?smiles=CN1C=NC2=C1C(=O)N(C(=O)N2C)C")
     assert response.status_code == 200
+    assert response.headers["content-type"] == "application/json"
     assert (
         response.text
         == '"[C][N][C][=N][C][=C][Ring1][Branch1][C][=Branch1][C][=O][N][Branch1][=Branch2][C][=Branch1][C][=O][N][Ring1][Branch2][C][C]"'